re: Github issue https://github.com/Unidata/netcdf-c/issues/1956
The function NC_compare_nc_types in libdispatch/dcopy.c uses an
incorrect algorithm to search for types. The core of this is the
function NC_rec_find_nc_type in libdispatch/dcopy.c. Currently
it searchs the current group and its subtree.
Additionally, the function NC4_inq_typeid in libsrc4/nc4internal.c
has been extended to handle fully qualified names. It was originally
designed to do this, but for some reason never completed.
The NC_rec_find_nc_type algorithm has been altered to match the
algorithm used by NC4_inq_typeid. It operates as follows.
Given a file F, group G and a type T. It searches file F2, group
G2, for another type T2 that is equivalent to T.
The search order is as follows.
1. Search G2 for a type T2 equivalent to T.
2. Search upwards in the ancestor groups of G2 for a type T2 equivalent to T.
3. Search the complete group tree of F2 in pre-order, breadth-first order to locate T2 equivalent to T.
Also add a test case to validate algorithm: ncdump/test_scope.sh.
Note, this change may cause compatibility problems, though it is
unlikely because two different equivalent type declarations in
one dataset is unlikely.
The netcdf-c code has to deal with a variety of platforms:
Windows, OSX, Linux, Cygwin, MSYS, etc. These platforms differ
significantly in the kind of file paths that they accept. So in
order to handle this, I have created a set of replacements for
the most common file system operations such as _open_ or _fopen_
or _access_ to manage the file path differences correctly.
A more limited version of this idea was already implemented via
the ncwinpath.h and dwinpath.c code. So this can be viewed as a
replacement for that code. And in path in many cases, the only
change that was required was to replace '#include <ncwinpath.h>'
with '#include <ncpathmgt.h>' and then replace file operation
calls with the NCxxx equivalent from ncpathmgr.h Note that
recently, the ncwinpath.h was renamed ncpathmgmt.h, so this pull
request should not require dealing with winpath.
The heart of the change is include/ncpathmgmt.h, which provides
alternate operations such as NCfopen or NCaccess and which properly
parse and rebuild path arguments to work for the platform on which
the code is executing. This mostly matters for Windows because of the
way that it uses backslash and drive letters, as compared to *nix*.
One important feature is that the user can do string manipulations
on a file path without having to worry too much about the platform
because the path management code will properly handle most mixed cases.
So one can for example concatenate a path suffix that uses forward
slashes to a Windows path and have it work correctly.
The conversion code is in libdispatch/dpathmgr.c, and the
important function there is NCpathcvt which does the proper
conversions to the local path format.
As a rule, most code should just replace their file operations with
the corresponding NCxxx ones defined in include/ncpathmgmt.h. These
NCxxx functions all call NCpathcvt on their path arguments before
executing the actual file operation.
In some rare cases, the client may need to directly use NCpathcvt,
but this should be avoided as much as possible. If there is a need
for supporting a new file operation not already in ncpathmgmt.h, then
use the code in dpathmgr.c as a template. Also please notify Unidata
so we can include it as a formal part or our supported operations.
Also, if you see an operation in the library that is not using the
NCxxx form, then please submit an issue so we can fix it.
Misc. Changes:
* Clean up the utf8 testing code; it is impossible to get some
tests to work under windows using shell scripts; the args do
not pass as utf8 but as some other encoding.
* Added an extra utf8 test case: test_unicode_path.sh
* Add a true test for HDF5 1.10.6 or later because as noted in
PR https://github.com/Unidata/netcdf-c/pull/1794,
HDF5 changed its Windows file path handling.
Without this define parallel netCDF-Fortran did not work
correctly with Open MPI, for example
examples/F90/simple_xy_par_wr.f90
reported
*** An error occurred in MPI_Info_dup
*** reported by process [2543714305,2]
*** on communicator MPI_COMM_WORLD
*** MPI_ERR_INFO: invalid info object
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
FixesUnidata/netcdf-fortran#109
The XArray implementation that uses Zarr for storage
provides a mechanism to simulate named dimensions.
It does this by adding a per-variable attribute called
_ARRAY_DIMENSIONS. This attribute contains a list of names
to be matched against the shape values of the variable.
In effect a named dimension is created with the name
_ARRAY_DIMENSIONS(i) and length shape(i) for all i
in range 0..rank(variable).
Both read and write support is provided.
This XArray support is only invoked if the mode value
of "xarray" is defined. So for example, as in this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,xarray,s3
````
Note that the "xarray" mode flag also implies mode flag "zarr", so the above
is equivalent to this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,zarr,xarray,s3
````
The primary change to implement this was to unify the handling
of dimension references in libnczarr/zsync.
A test for this and other pure-zarr features was added as
nczarr_test/run_purezarr.sh
Other changes:
* Make sure distcheck leaves no files around.
* Change the special attribute flag DIMSCALEFLAG to HIDDENATTRFLAG
to support the xarray attribute.
* Annotate the zmap implementations with feature flags such as
WRITEONCE (for zip files).
re: Issue
The netcdf dispatch table version was defined in several places.
Modify to only require defining it in CMakeLists.txt and configure.ac.
Fix entailed the following changes:
* Up the NC_DISPATCH_VERSION from 2 to 3 in configure.ac and CMakeLists.txt
* Create include/netcdf_dispatch.h.in and use it to configure include/netcdf_dispatch.h
* For CMAKE, make it search CMAKE_CURRENT_BINARY_DIR so code can locate the configured netcdf_dispatch.h
* Add entry to config.h.cmake.in for NC_DISPATCH_VERSION
* Move NCerror from include/ncdispatch.h to libdap2/nccomon.h
* Fix an API problem re nchttp.h
* Fix a conversion warning in libdispatch/dinfermodel.c
re: Issue https://github.com/Unidata/netcdf-c/issues/1936
The algorithm controlling interaction of -d 0 -F and -c / options
is incorrect.
The fix:
1. make -d 0 => no deflation
2. make -F properly use the filter specs to decide.
Also added a test case to ncdump/tst_nccopy4.sh.
The primary change is to support the use of a zip file as a
storage format. Simultaneously the .nz4 support is made obsolete
Use of zip requires the libzip support library, so a number of
changes to the build files (Makefile.am, CMakeLists.txt) are
necessary to locate and incorporate libzip. The nczarr_tests
tests are also changed to add zip testing.
Other changes:
* Make sure distcheck leaves no files around.
* Add some functions to netcdf_aux to export some functions of libnetcdf.
* Add a new error NC_EFOUND as the complement of NC_EEMPTY.
* Add tracing support to nclog and use it in libnczarr.
* Modify the zmap interface to support the writeonce semantics of zip.
* Create a new s3util.c to support a variety of S3 auxilliary functions.
* EXTERNL'ize a number of functions so they can be used in s3util.
* Add support for the S3 ListObjects CommonPrefixes mechanism
to improve search.
* Add experimental support for running nczarr X s3 tests against
the actual Amazon S3 cloud.
Changes:
1. add "use_nczarr: [ nczarr_off, nczarr_on ]" to matrix
2. add libzip-dev to the apt installs (might need caching).
3. convert deprecated "--enable-netcdf-4" to "--enable-hdf5" (also for cmake)
